Lilly's son!
by Romantific
Summary: Hogwarts is in for a shock this year, Professor Snape will get the shock of his life along with the rest of the wizarding world and Albus Dumbledore gets knocked off his high horse. As things are revealed one question will be on everyone's mind, is Harry Potter the real prophecy child and what really happened that night? Contains M/M, mentions of abuse and autism.
1. Chapter 1

**Lilly's son!**

 **Disclaimer:** I do not own Harry Potter!

 _This story contains child abuse which I don't condone as I have suffered from it myself and Autism which I know a fair bit about as my younger sister has mild Autism. It is all fact._

 **Chapter: 1**

"Minerva, have you received all the school reports for the muggle raised students yet?" Headmaster Albus Dumbledore asked from his place at the large table in the staff room where he and the four house heads were gathered for the first meeting of the year. This meeting was being held to discuss the new students due to start their first year of Hogwarts in September to discuss any potential issues with the new students 'mainly muggle-borns and muggle raised) and hash out plans to help them when they are sorted into their houses.

Minerva lifted her head from the file she was currently frowning at in concern and glanced at the other occupants of the room, eyes lingering on the ever scowling potions master before turning her attention back to the headmaster and nodding.

"I've been through all the files and all have returned their acceptance letters bar one…" She paused for a moment glancing back at the file. "This student is currently enrolled in a muggle primary school and has better grades then even those years above him, however his file is slightly concerning. The student was diagnosed with Autism in his first year and all of his teachers have filed a complaint with child protective services reporting suspected abuse with nothing ever coming from it as they had no proof and the poor child doesn't understand that the way his guardians are treating him is wrong so therefore is uncooperative. The school nurse has noted multiple broken bones and suspicious bruises along with malnourishment and is a lot shorter than other students his age. When the guardians of this boy are questioned about these things, they immediately brush it off as clumsiness and the child returns to school the next day with new bruises."

"Is the boy verbal?" Professor Snape questioned scowling darkly thinking back to his own abusive childhood and vowing to help the child as no child not even James Potter deserved that. How he loathed that man even now that he was dead. He was often the brunt of Potters pranks and insults when they were in school together and he swore to help any and all children who suffered like he had. He was also the reason he lost the love of his life, his soulmate.

"He has a high grasp of the English language and is smart well beyond his years but often gets confused with the way people word things and takes everything literally. Say for instance if Madame Hooch were to say to the class leave your brooms where they are as she is finishing the class or taking a child to the infirmary and he still had it in his hand he would take that literally and still fly around on the broom without supervision or walk off with the broom still in his hand and argue the point when told off for not listening to the teacher because she hadn't specifically said put your brooms on the ground or no flying without adult supervision because he doesn't understand the meaning behind what she has said. Apparently he loves rules and any deviation from his schedule results in a meltdown. He doesn't like to be touched and refuses to look people in the eye often looking at the forehead, nose, over the shoulder of the person he's talking to or at the ground. He has trouble with his motor skills find writing very difficult and often gets frustrated as he is unable to grip the pencil correctly to write with. When excited or upset he flaps his hands or twists them while rocking on his feet, he uses his hands as a form of communication. He is a very polite and kind child generally but when he has a meltdown it can be explosive, hurting himself, throwing himself of the ground screaming and the only way to bring him out of it is to grip him in a tight bear hug and talk to him about the problem until he calms down. According to this he absolutely loathes the colour green and one of the students in his art glass had thrown green paint on him and he had the biggest meltdown any of the teachers had ever seen and it took a good half an hour to calm him down which included him scrubbing himself raw in the showers and a change of clothes. He had refused to even take them home stating 'green is bad, green hurts' and he also has a problem with large groups of people being too close to him and loud noises spook him. He doesn't like the Unknown and needs every new thing described in detail before he will do it, he needs to know what is going to happen otherwise he gets overwhelmed and goes to hide somewhere to calm himself." Silence met her as she finished her in depth report.

"And this child is enrolled at Hogwarts but hasn't answered his acceptance letter? What's his name." The headmaster questioned while stroking his beard deep in thought.

Minerva turned and looked right at the unusually solemn potions master and answered.

"It's Harry Potter." His eyes grew wide in shock.

"You're….. You're joking right?" He choked out.

She shook her head "I wish I were."

"Severus I know you're past with his father but…" Severus cut him off.

"My past with his father has nothing to do with it Albus, I'm not so heartless as to take my hate out on a defenceless and disabled little boy who doesn't understand the reasoning behind it. I will help him as much as I can as I have experience with Autism. My cousin from my fathers side has high functioning Autism, I know what to expect." He scowled at the headmaster for even thinking such a thing. He bowed his head apologetically.

"Forgive me Severus, I didn't mean to insult you. Now, I would like for you to visit his house and see for yourself if anything his going on as you have the most experience with this sort of thing and if you find anything I want you to grab him immediately and bring him here and I will have to figure out an appropriate guardian for him during the holidays." Severus nodded and stood.

"I will do that now, if what that report says is true then I want him out of that place immediately." With that he swept out of the room with his cloak billowing behind him as he rushed back to his quarters to change into some muggle clothing before leaving the school and appearing in front of a house on Private Drive in Surrey that had him sneaking in disgust at the mundaneness of all the houses looking exactly alike.

Shaking his head he stalking across the road until he reached number four before rapping sharply on the door which opened moments later to reveal a horse faced blonde woman whose eyes widened in recognition before narrowing. "YOU!" She snarled at Severus who smirked.

"Hello Tuney, long time no see….."


	2. Chapter 2

**Lilly's son!**

 **Disclaimer:** I do not own Harry Potter!

 _This story contains child abuse which I don't condone as I have suffered from it myself and Autism which I know a fair bit about as my younger sister has mild Autism. It is all fact._

 **Chapter:2**

 _"YOU!" She snarled at Severus who smirked._

 _"Hello Tuney, long time no see….."_

They stood there glaring at each other for a moment before the were interrupted by the largest man Severus had ever seen.

"Who's there pet?" His beady eyes roaming over Severus before turning his attention back to his wife.

"He's one of his kind." She sneered as she moved to slam the doors in his face. Severus moved quickly, forcing the door open and letting himself in.

"Get out of my house you freak we don't want your kind here." Vernon shouted, chins wobbling and face going a deep purple and Severus could feel his patience quickly running out.

"I'm here for Harry. You needn't worry, he won't be coming back here again." He told them as he pushed his way through the door and headed for the living room. "Call him down here now so we can leave, I don't want to be here any longer than I need to." He sneered as he stood by the stairs looking expectantly at Petunia.

"You can't have him, he's ours. We swore when we took him in that we'd put a stop to this nonsense." Vernon thundered as he stomped toward Severus who pulled out his wand and calmly twirled it in his fingers.

"Bring me the boy now, or I'll use your son as a Ginini pig for a potion experiment I'm in the middle of." He said staring at Petunia again who was glancing nervously at Vernon out of the corner of her eye then at Severus and then the cupboard under the stairs pointedly mouthing the words 'knock him out' at the same time.

"You will leave my house this instant or I'll call the police." He roared at Severus who just sent a stunner his way before turning back to Petunia raising an expectant eyebrow at her.

"There's something you need to understand before we continue, I love my nephew. He's all I have left of my sister and I tried to protect him the best I could from Vernon. Now that you are here for him I can take Dudley and leave, you cannot let him come back here I'm afraid Vernon will kill him soon. I have a letter from Lilly and a trunk full of her possessions in the attic, you need to read the letter before you take him. It will explain a lot. The trunk is for both you and Harry." She told him as she moved quickly to the stairs where she disappeared before returning with the trunk and the letter before handing them both to Severus who let out a shaky breath as he sat down to read the letter.

 _My dearest Severus,_

 _If you are reading this then I failed in my task and for that I am so sorry my love._

 _I had meant to do this in person once it was safe for Harry and I to be in the open again, but I guess that was just not meant to be. I never meant to hurt you Sev, and I'm so sorry that you are going to be hurting even more once this letter is through. I never cheated on you Severus, that's just what Dumbledore wanted you to believe. Harry is your son, our son. Dumbledore knows this and is the reason I went into hiding with James. He told me that you were in grave danger and so was Harry, how he knew I was pregnant I will never know because I didn't yet. The prophecy is fake, the dark lord found this out and offered Harry and I protection. There is a reason Dumbledore tried to send the dark lord after us and he was trying to figure what that was. If I died, it wasn't at the hands of the dark lord. What we were lead to believe about him was wrong, I saw it all for myself. I want you to promise me Severus that you will find a way to bring the dark lord back and help him defeat Dumbledore and protect our son. Voldemort is about equality, bringing back the old ways and keeping our worlds separate. He is right, us muggleborns have all but destroyed this world and it needs to change back to the way it was before we die out. Without the old ways being practiced magic is dying, each generation of witch and wizard is getting weaker and it must be stopped or before long there will be no magic left only squibs and muggleborns. Dumbledore is not who he tries to make out to be, James went into hiding with me to protect us. In doing so we not only failed but we let Dumbledore win and hurt you in the process. I'm so sorry._

 _In the trunk you will find Harry's birth certificate with your name on it, take it to Gringots. They will know what to do, Harry is still the Potter heir as James named him heir when we went into hiding just in case we didn't survive. You will have access to all of this as Harry's father and magical guardian._

 _I must go now, take care of our baby for me. I love you both with all my heart and will be waiting for you on the other side._

 _Forever and always,_

 _Lilly._

Severus sat there for a few moments before opening the trunk to find the birth certificate sitting on top of everything else. He reverently picked it up and opened it with shaky hands.

 **Name:** _Harrison Severus Prince-Snape_

 **D.O.B:** _31st July 1999_

 **Father:** _Severus Tobias Prince-Snape_

 **Mother:** _Lilly Maree Evans_

 **Godfather:** _Lucius Abraxas Malfoy_

 **Godmother:** _Narcissa Rose Malfoy née Black_

 **Heir:** _Prince_

 _Snape_

 _Potter_

 _Evans_

Severus just sat there staring at the letter and certificate in his shaking hands with tears in his eyes. "Oh god, he's my son." He sobbed.

"I'm sorry Severus, I tried to contact you when I found Lilly's letter to me but it always came back unopened so I tried my best to protect him from my position. I would have left Vernon sooner but I had no way to support the three of us and I couldn't leave my son with him. I just hope you, Lilly and Harry can forgive me one day for not being stronger."

"Where is he, where's my son?"


	3. Chapter 3

**Lilly's son!**

 **Disclaimer:** I do not own Harry Potter!

 _This story contains child abuse which I don't condone as I have suffered from it myself and Autism which I know a fair bit about as my younger sister has mild Autism. It is all fact._

 **Chapter:3**

"Where is he, where's my son?" He asked looking up gaining control of his emotions. "Dumbledore will pay for this." He said as Petunia moved towards the cupboard under the stairs and opened the door.

"Harry, there's someone her to see you. He's going to take you away from here and keep you safe, remember what we talked about?" She said softly.

"Father knows now, fathers here." He said as he rocked back and forth on his heels.

"That's right Harry, your father knows now and he's here. Can you come out and say hello please?" She asked holding her hand out to the small boy who took her hand as she pulled him from the cupboard and lead him to Severus who frowned at the sight he made.

Harry was very small for his age and looked more like a nine year old who was a carbon copy of James Potter without the glasses and with Lilly's eyes.

 _"Finite incantartum."_ He muttered as he wavered his wand over Harry who's appearance automatically changed. His hair became a tame shoulder length black with red highlights throughout in a mixture of both parents, his skin complexion changed from a healthy tan colour to a milky white though his height and build stayed the same from the malnourishment.

"Hello Harry, my name is Severus Snape. I'm your father, I'm so sorry that I didn't come sooner." He whispered as he drank in his sons features.

"Didn't know." Harry muttered looking at a point over Severus's shoulder.

"Can you say hello to your father Harry?" Petunia encouraged running a hand through his hair.

"Hello father, my name is Harry."

"Hello Harry, It's nice to meet you. I need you to say goodbye to your aunt for me please. We have a lot to do today before I can take you back to Hogwarts so we need to get moving okay?" He asked softly.

"By aunt Petunia." Harry muttered as he looked at the open trunk in front of his father. "Mine." He whispered as he picked up a beautiful plush soft doe cuddly toy with green eyes. "Lilly." There was another that he pulled out with onyx eyes. "Sev." He said as he showed them to the two adults who were staring at him in shock.

"He knows nothing of his past, we never told him." Petunia whispered with tears in her eyes as the implications where made clear.

"He remembers what happened that night, oh Harry I'm so sorry if I had known I would have been there." Severus whispered trying to contain the urge to cry out in despair. "Come, I will take you to Gringots to get this sorted out and get you out of Dumbledore's control the we'll shop for your things and I'll take you to meet your godparents." He put the doe's back in the trunk and shrunk it to fit in his pocket and placed the certificate and letter in his breast pocket then took Harry's hand before turning to Petunia once more. "Thank you for trying to protect him, you needn't worry about money to support yourself and your son as I will be opening a bank account in your name and the deed to my house in Spinners end will be changed into your name. Twixi!"

"Yes master Severus?" The little elf answered as she popped in startling Harry who freaked out and hid behind his father for protection against the mysterious creature.

"It's alright Harry, this is Twixi my house elf. Twixi this is Harry, my son." He introduced them making Harry relax slightly and just stare at the creature quietly. "Your job will be to look after him and take him straight to Lucius if I am not near him even if he's at Hogwarts you are to take home and only return him when I call you. I will visit Lucius and inform him once I'm finished with my affairs today. For now I want you to clean out Spinners end and get it liveable for Mrs. Dursley and her son as fast as you can please. Leave the keys in the letter box for her then take all the elves to Prince manor when you are done as we won't be returning there. Understand?"

"Yes sir, Twixi be doing that right away sir." The little elf saluted before popping back out again.

"You don't need to do this for me Severus." Petunia protested.

"I know that, nobody deserves to be stuck with that beast and I refuse to let my sons aunt, my soulmates only sister to become like my mother." He said pulling out his wand again. "Accio Petunia and Dudley's belongings." Everything belonging to said people came flying into the room and gently lowered itself into the bottomless trunk that he summoned for their things. When it was done he shrunk it and put a feather light charm on it before hand it over to petunia. "Put it in your pocket, it will resize when you put it on the ground. Take your can and go and get your son from school and drive straight to my old house, do you remember where it is? Good, if you need anything call for Twixi who I will send with your new bank card and account details. Good luck." He held Harry's hand tightly. "Hold on tight understand. It's going to feel like you're being sucked through a straw and it will make you feel ill but I will give you something to fix that. Do not let go understand?" He asked Harry who nodded.

"Yes father, I understand. Goodbye aunt Petunia."

"Goodbye Harry, good luck." She smiled as Severus apparated them to the Leaky Cauldron and quickly led him through the pub and out the back to the entrance to the alley.

"Here Harry, drink all of this it's an anti nausea potion. It will taste horrible but it will stop you from feeling sick okay?"

"Okay." Harry repeated as he gulped the potion down and shuddering as Severus once again pulled out his wand to tap the pattern on the bricks to gain entry to the alley. Once they were through Severus quickly led his son to the bank and asked for a private room and the manager of the Prince and Potter estates immediately while he explained to his son what the goblins were and to remain quiet and only speak when asked a question for his safety.

"What can we at Gringots do for you Lord Prince?" Ironclaw, the Prince estate manager asked as the were all seated.

"I would like to claim custody of my son and file a lawsuit against Albus Dumbledore…."


	4. Chapter 4

**Lilly's son!**

 **Disclaimer:** I do not own Harry Potter!

This story contains child abuse which I don't condone as I have suffered from it myself and Autism which I know a fair bit about as my younger sister has mild Autism. It is all fact.

 **Chapter: 4**

"Claiming custody of your son will be easy enough as we already had the paperwork prepared for this day at the request of miss Evans. All that is required is a blood test and then your signature." Ironclaw told him and Severus nodded before turning to his son.

"Harry, we need to give your finger a little cut to take some blood to prove that I am your father. Are you ok with that?" He asked gently whilst taking his sons hand again.

"Ok with that." Harry repeated and glanced at him before going back to counting the tiles on the walls.

"It will hurt a little bit but I will heal it right away." The goblin pulled out the paternity potion and poured it in a glass bowl before handing Severus the dagger. He quickly made the cut and squeezed Harry's finger to get the required 3 drops and getting a muttered 'ow' for his efforts before he healed his sons finger and gave his own 3 drops of blood to the potion. It glowed a bright green proving him to be Harry's biological father and he let out the breath he didn't even know he had held in until then.

"Now that's taken care of I will need you to sign here with this blood quill and the boy will be yours completely." He told him as he added the results of the test to the papers and it was done. Harry was officially his.

"As for the charges against Dumbledore, I would advise against it for the time being. You need to lay low and bring back the opposition whilst beating him at his own game. I have made sure that no matter what he tries, he will never get custody of your son again and if something were to happen to you he would automatically go into the custody of his godparents Lucius and Narcissa Malfoy unless you decide otherwise." Severus shook his head.

"No, I have no problem with them caring for my son. Lucius is a good man and has a son of his own." Ironclaw nodded.

"Now as for the Potter Estate, Dumbledore fancied himself as young master Snape's magical guardian and tried to enter the main Potter vault but was denied and any outgoing money at the time was stopped the moment Lord Potter died. The only transactions still currently outgoing were personally stated to be left that way by Lord Potter himself and may only be stopped by the Potter heir. Young master Snape was officially named heir when miss Evans and Lord Potter went into hiding with the stipulation that should Lord Potter live through the war and produced a son the title would revert back to the rightful owner. Since that never happened young master Snape is officially the heir to the Potter fortune and you as his father and magical guardian have full control over the accounts. Money incoming from various businesses are substantial enough to cover the outgoing coat times three. Would you like to see the statements?" He asked Severus who shook his head, still reeling from the information he was just given.

"No, just tell me who the money is going out to please."

"Very well, money is placed into various businesses like broom companies and the like and there are two charity programs also signed off by Lord Potter. One is for St Mungo's hospital and the other is a bird watchers charity." Severus sat forward at the last one.

"That's Dumbledore's order."

"Might I suggest you leave it for the time being to curb suspicions until the Dark Lord has returned, he must think that the worst thing to have happened is you learning of your son and taking custody of him. Now if that is all, we both have a lot of work to do. Good day masters Prince-Snape." Ironclaw concluded, practically shooing them out the door.

"Come Harry, you're going to meet your godfather now. We will need to apparate again ok, I will have another nausea potion ready for you." He told him as he stood and helped Harry to his feet.

"You may use the floo if you'd like." Ironclaw offered.

Severus nodded. "That would be better, thank you for your help Ironclaw. May your enemies fall at your feet."

"May your vaults always prosper." He returned.

"Alright Harry, same as before. Hold on and don't let go alright?"

"Hold on and don't let go alright." Harry repeated.

"Malfoy Manor, Ivory." Severus shouted out the password and in a flash of green flames they were gone. On the other side Harry was pretty much having a meltdown.

"Bad, that was bad. Dirty, don't like dirt. Bad, bad, bad." He chanted as he rocked back and forth as he scratched at the dirt on his clothes and started to hit himself on the head as he couldn't get the dirt to come off. Severus quickly threw a cleaning spell at his son and grabbed his hands to stop him from hurting himself as he Knealt in front of him.

"Alright Harry, that was bad and we won't do it again ok? Look, no more dirt, it's gone, you're clean again." He lifted one of Harry's hands to show him and repeated what he said until Harry finally heard him and was listening to him.

"Clean." Harry inspected his hand and threw q quick glance at his father. "No more dirt!" He told him.

"No more dirt!" He promised.

"White man." He muttered as he quickly glanced over his fathers shoulder then around the roofing a few times.

"That's my best friend, his name is Lucius. He's like my brother." Severus explained to the boy in front of him as he tried to regain his attention.

"Brother?" Harry tilted his head adorably.

"Yes, my brother. He's your godfather and will look after you if I can't ok?"

"White tall man, uncle." He muttered.

"Yes, you're uncle." He told him as he stood and turned to face Lucius who stood in the doorway looking seriously confused.

"What's going on Severus?" He asked quietly as he lead them both to the living room.

"This is Harrison Severus Prince-Snape formerly known as Harry James Potter." As he spoke Lucius' eyebrows blended further and further into his hairline. "He's my son!"


End file.
